The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

Abstract

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.

Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes

“…( 98 ), showed that fgf3 is expressed in developing pufferfish dermal spines. Given this and a trove of other evidence for an FGF signaling role in the development and diversification of scales, spines, and denticles in ray-finned and chondrichthyan fishes ( 96 – 102 ), absence of fgf3 and fgf4 in the often heavily armored, elaborately spined syngnathids clearly suggests that derived mechanisms for integumentary bone development are at play in this lineage.…”

Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes

“…Shono et al, (Shono et al, 2019), showed that fgf3 (and fgf1a) are expressed in developing pufferfish dermal spines. Given this and a trove of other evidence for an FGF signaling role in the development and diversification of scales, spines, and denticles in ray-finned and chondrichthyan fishes (Albertson et al, 2018;Aman et al, 2018;Cooper et al, 2017;Cooper et al, 2018;Daane et al, 2016;Kim et al, 2019;Shono et al, 2019), absence of fgf3 and fgf4 in the often heavily armored, elaborately spined syngnathids clearly suggests that derived mechanisms for integumentary bone development are at play in this lineage.…”

Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di)

“…Recent advances in genomic tools have been proven to be very useful not only for ecological and evolutionary studies but also for the agricultural sciences. Notably, developments in various high-throughput cost-effective genotyping-by-sequencing (GBS) systems, such as RADseq (and its derivatives) (Baird et al 2008 ; Peterson et al 2012 ; Andrews et al 2016 ), MIGseq (Suyama and Matsuki 2015 ), and Ampliseq (Sato et al 2019 ), facilitate a wide range of genetic analyses, including population structure analysis (Hohenlohe et al 2010 ; Cavender-Bares et al 2015 ; Hirase et al 2020 ), linkage map construction (Elshire et al 2011 ; Hoshino et al 2016 ; Escudero et al 2018 ), and forward genetics (Wilson et al 2014 ; Zhou et al 2015 ; Ieda et al 2018 ; Kim et al 2019 ), even for non-model organisms. These technologies are also recognized as powerful tools for aquaculture studies, as they are utilized in the implementation of selective breeding programs and the management of genetic diversity of target populations (Houston et al 2012 ; Palaiokostas et al 2013 ; Hosoya et al 2018 ).…”